WASHINGTON — Far from California’s San Joaquin Valley, an irrigation drainage problem that once turned deadly continues to confront a crucial but little-known federal court.

Though the U.S. Court of Federal Claims recently dismissed a $1 billion claim brought by the Westlands Water District, the nation’s largest, individual Westlands farmers are proceeding with a separate lawsuit filed in the same court. The legal arguments are different, but the stakes seem equally high.

“This is a constitutional claim, on behalf of individual farmers who are hurting,” Gus B. Bauman, an attorney involved in the case, said Wednesday. “The bottom line is, there has been a war going on in California . . . and the people who are getting hurt are the farmers who relied on government promises.”

Bauman is one of the attorneys for Mendota, Calif.-area farmer Michael Etchegoinberry and three other others who are challenging the government. The farmers hope that in time a judge certifies their case as a class action, which would crank up the pressure.

The farmers argue that the federal Interior Department’s failure to build a promised drainage system effectively rendered their privately owned land useless. They contend that this amounts to a taking, for which the federal government must pay.

The previously unreported lawsuit by the farmers as well as Westlands’ separate legal action, dismissed last week, center on the federal government’s failure to provide a drainage system for the valley’s west side. As a result, used and salty irrigation water accumulates and threatens valuable cropland.

Federal officials once directed the drainage to the Kesterson National Wildlife Refuge in western Merced County. Because the planned drain was never completed the additional 107 miles to the Sacramento-San Joaquin Delta, the toxic buildup at Kesterson Reservoir poisoned wildlife. At least 1,000 migrating waterfowl died from 1983 to 1985 through exposure to the selenium-tainted Kesterson water, federal officials later estimated.

Farmers, too, have suffered from the lack of irrigation drainage to accompany the delivery of irrigation water provided at subsidized prices. High water tables cause problems, ranging from stunted crops to decreased yields and sterile land.

Justice Department attorneys respond that Etchegoinberry and other Westlands farmers filed their lawsuit too late, since they should have known long ago about the drainage problems.

“Since closure of the Kesterson Reservoir in June 1986, no drainage service has been provided by the United States to any landowner in the Westlands Water District,” Justice Department attorney E. Barrett Atwood wrote in a brief. “From that point forward, there can be little doubt that landowners in Westlands knew that damage was occurring, and could continue to occur to their farmlands because they continued to irrigate but did not have drainage.”

Multiple lawsuits going back many years so far have failed to provide a permanent drainage solution for farmers in the 600,000-acre Westlands Water District. The latest lawsuits filed at the court of claims represent a relatively new front in the long-running fight.

Westlands sued last year under the theory that the federal government had breached a contractual obligation to provide drainage service. But in a ruling Jan. 15, Judge Emily C. Hewitt concluded that Westlands “failed to show that drainage service was a bargained-for benefit of any of these contracts” and dismissed the suit.

Though the water district isn’t party to the Etchegoinberry lawsuit, it helps the funding of it through a special fee assessed on farmers whose land has suffered from the lack of drainage.

The next anticipated turning point in the Etchegoinberry case will be a judge’s ruling on the Justice Department’s request to dismiss it.

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